Recent Scientific Developments in Genetics, Genomics, and Breeding of Fruit Trees

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Collection Editor
Hainan Provincial Key Laboratory of Quality Control of Tropical Horticultural Crops, School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
Interests: regulation and molecular mechanism of fruit quality
Special Issues, Collections and Topics in MDPI journals

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Collection Editor
School of Food Engineering, Ludong University, Yantai 264011, China
Interests: fruit quality; transcriptional regulation; regulation of gene expression
Special Issues, Collections and Topics in MDPI journals

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Collection Editor
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: fruit germplasm resources and genetic breeding; fruit quality; secondary metabolism; light and hormone signal response; transcriptional and epigenetic regulation

Topical Collection Information

Dear Colleagues,

Fruit trees are cultivated all over the world due to their great economic value. In recent years, the increasing demand for high-quality fruit with high resistance to pests and diseases has tremendously promoted the development of fruit tree research. However, detailed functional analyses of fruit trees are far behind model plants, due to highly heterozygous and complex genomes and the barrier of plant genetic transformation and/or regeneration in some fruit tree species. Fortunately, the application of next-generation sequencing technologies coupled with rapid advances in bioinformatics has facilitated the development of fruit trees for genetic and genomic studies as well as molecular breeding over the last decade. Furthermore, the development of gene-editing technologies, such as CRISPR-Cas9, allows for their application in the study of fruit tree genetics and breeding.

The proposed Topical Collection entitled “Recent Scientific Developments in Genetics, Genomics, and Breeding of Fruit Trees” aims to present advances in gene mining, genetic mechanisms, omics analyses (e.g., genomics, transcriptomics and proteomics), and the application of gene-editing technologies and molecular breeding of fruit trees. We look forward to receiving your manuscripts (including reviews and research articles) and are eager to share your newest findings.

Dr. Minjie Qian
Dr. Aidi Zhang
Dr. Junbei Ni
Collection Editors

Manuscript Submission Information

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Keywords

  • fruit trees
  • molecular breeding
  • genotyping and phenotyping
  • bioinformatics
  • comparative genomics
  • QTL mapping
  • genome-wide association studies
  • transcriptome analysis
  • gene editing
  • gene function

Published Papers (9 papers)

2025

Jump to: 2024, 2023, 2022

20 pages, 1359 KiB  
Review
The Origin, Applications, and Breeding Goals of Jujube in China
by Menghan Wu, Yaoxi Liu, Tingjian Jiang, Yiteng Liu, Zhuo Chen, Xiaofei Wang, Huafeng Yue, Fangdong Li, Gaopu Zhu and Mengmeng Zhang
Horticulturae 2025, 11(1), 37; https://doi.org/10.3390/horticulturae11010037 - 3 Jan 2025
Cited by 1 | Viewed by 1094
Abstract
Jujube (Ziziphus jujuba Mill.) is one of the three traditional woody crop species in China, where it originated from the middle and lower reaches of the Yellow River. Jujube is considered one of the oldest cultivated fruit trees species in the world, [...] Read more.
Jujube (Ziziphus jujuba Mill.) is one of the three traditional woody crop species in China, where it originated from the middle and lower reaches of the Yellow River. Jujube is considered one of the oldest cultivated fruit trees species in the world, as its utilization can be traced back to more than 7000 years ago. The jujube has important nutritional, economic, and ecological values, hence it is well received by both planters and consumers. At present, jujube cultivation has spread to more than 48 countries and provides a pathway for Chinese farmers to produce a lucrative cash crop. Jujube is regarded as a superfruit of the future due to its excellent nutritional profile. Social progress and economic shifts leading to the improvement of living standards influence the value of jujube to consumers, who have gradually shifted toward functional foods, while at the same time, consumer desires and environmental pressures change the breeding goals for new jujube varieties. In this review, we summarize the origin, classification, and historical, as well as modern, uses of jujube. We also provide some advice on the establishment of breeding objectives in this new period of jujube development. This review aims to provide useful references for researchers new to jujube, to guide shareholders in the jujube industry, and to formulate breeding objectives for the modern development of elite jujube cultivars. Full article
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22 pages, 7354 KiB  
Article
Cytokinin Oxidase (CKX) Family Members in ‘duli’ (Pyrus betulifolia Bunge): Genome-Wide Identification and Tissue Expression Profile Under Abiotic Stress
by Weimin Wang, Ting Xie, Jiaojiao He, Kuozhen Nie, Zijuan He, Yuxing Zhang and Yingli Li
Horticulturae 2025, 11(1), 29; https://doi.org/10.3390/horticulturae11010029 - 2 Jan 2025
Viewed by 677
Abstract
Cytokinin oxidases/dehydrogenases (CKXs) play a crucial role in modulating plant stress resistance by degrading cytokinins. The ‘duli’ pear (Pyrus betulifolia Bunge), a highly stress-resistant cultivar, is widely used as a rootstock in pear cultivation. This study aims to comprehensively identify and [...] Read more.
Cytokinin oxidases/dehydrogenases (CKXs) play a crucial role in modulating plant stress resistance by degrading cytokinins. The ‘duli’ pear (Pyrus betulifolia Bunge), a highly stress-resistant cultivar, is widely used as a rootstock in pear cultivation. This study aims to comprehensively identify and characterize the PbCKX gene family in ‘duli’. A total of 10 PbCKX genes were identified, which are unevenly distributed across five chromosomes and classified into four groups based on sequence similarity and phylogenetic relationships. The PbCKX genes exhibit a high degree of conservation in motifs and structural features, although exon structure variations are observed. Comparative analysis revealed 10 homologous gene pairs between ‘duli’ and Arabidopsis and 14 pairs between ‘duli’ and apple. Additionally, cis-acting elements related to abiotic stress, hormone responses, and light responsiveness were identified in the promoter regions of the PbCKX genes. RNA-seq analysis showed that PbCKX1 and PbCKX2 were predominantly expressed in roots, while PbCKX3 to PbCKX10 had higher expression in leaves. The PbCKX genes responded to both exogenous hormones and salt stress, with salt stress inducing a more pronounced response. Most abiotic stress treatments led to the downregulation of PbCKX4 and PbCKX9, while PbCKX6 and PbCKX8 were upregulated. Notably, treatments with Abscisic acid and NaCl significantly enhanced CKX enzyme activity in ‘duli’ over 20 days, reducing levels of zeatin and isopentenyladenine. Conversely, treatments with gibberellin, cytokinin, and auxin significantly reduced CKX enzyme activity and increased concentrations of zeatin and isopentenyladenine over the same period. These findings provide valuable insights for future studies on the functional role of PbCKX genes in abiotic stress responses in ‘duli’. Full article
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2024

Jump to: 2025, 2023, 2022

20 pages, 10163 KiB  
Article
Genome-Wide Identification of Litchi SPL Gene Family and Expression Analysis in Pericarp Anthocyanin Biosynthesis
by Ziqiang Xu, Jiayun Wu, Xiangyang Jing, Faiza Shafique Khan, Yanzhao Chen, Zhe Chen, Hongna Zhang and Yongzan Wei
Horticulturae 2024, 10(7), 762; https://doi.org/10.3390/horticulturae10070762 - 18 Jul 2024
Cited by 1 | Viewed by 1529
Abstract
During the ripening of litchi (Litchi chinensis Sonn.) fruit, anthocyanin biosynthesis is crucial in providing vibrant coloring. Previous studies on anthocyanin-related transcription factors have made significant discoveries relating to plants. However, the role of the SQUAMOSA promoter-binding protein-like (SPL) [...] Read more.
During the ripening of litchi (Litchi chinensis Sonn.) fruit, anthocyanin biosynthesis is crucial in providing vibrant coloring. Previous studies on anthocyanin-related transcription factors have made significant discoveries relating to plants. However, the role of the SQUAMOSA promoter-binding protein-like (SPL) transcription factors in anthocyanin biosynthesis has rarely been studied in litchi. SPL genes are widely involved in the developmental mechanisms of plants. In this study, a total of 17 SPL genes have been identified from the litchi genome. Phylogenetic analysis revealed that these genes were divided into eight groups (Group I-VIII). Analysis of gene structure conserved domains, conserved motifs, and miR156 target prediction showed that LcSPLs were highly conserved during evolution. RNA-seq analysis of litchi revealed that six LcSPL genes have a role in regulating anthocyanin biosynthesis. Further, weighted correlation network analysis (WGCNA) revealed LcSPL7’s role in anthocyanin synthesis and chlorophyll degradation in litchi fruit ripening. These findings collectively suggest that the LcSPL gene family plays an essential role in anthocyanin biosynthesis in litchi pericarp. In summary, comprehensive bioinformatics analysis of the SPL family expands our understanding of anthocyanin synthesis in litchi pericarp. Full article
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17 pages, 13038 KiB  
Article
Genome-Wide Identification and Analysis of the Nuclear Factor Y Gene Family in the Woodland Strawberry Fragaria vesca
by Yang Zhou, Feiyan Gao, Wenjie Zhao, Tianjia Liu and Mengzhao Wang
Horticulturae 2024, 10(7), 755; https://doi.org/10.3390/horticulturae10070755 - 17 Jul 2024
Cited by 1 | Viewed by 1465
Abstract
Nuclear factor Ys (NF-Ys) are heterotrimeric transcription factors that specifically bind to CCAAT boxes present in numerous eukaryotic promoters. In plants, NF-Y proteins consist of the following three subunits: NF-YA, NF-YB, and NF-YC, each encoded by a gene family. Accumulating [...] Read more.
Nuclear factor Ys (NF-Ys) are heterotrimeric transcription factors that specifically bind to CCAAT boxes present in numerous eukaryotic promoters. In plants, NF-Y proteins consist of the following three subunits: NF-YA, NF-YB, and NF-YC, each encoded by a gene family. Accumulating evidence underscores the crucial roles of NF-Y proteins in various plant development processes and stress responses, such as embryogenesis, flowering time control, drought tolerance, and heat tolerance. Despite this, a comprehensive genome-wide overview of the NF-Y gene family in strawberries is lacking. To bridge this gap, this study was conducted to identify and characterize the NF-Ys in Fragaria vesca. The investigation revealed the presence of six NF-YA, twelve NF-YB, and five NF-YC members in F. vesca. Furthermore, a comprehensive analysis of the FveNF-Ys was performed, including their phylogenetic relationships, gene structures, chromosomal locations, and conserved domains. MiRNA target site prediction found that there were 30 miRNA target sites in 12 (52.2%) FveNF-Y genes. Additionally, the expression profiles of different tissues and developmental stages demonstrated tissue-specific expression patterns among certain members of each NF-Y subfamily. This observation suggests that specific NF-Y subfamily members may play unique roles in different tissues or stages of development. Furthermore, the transient expression assay demonstrated that three selected FveNF-Ys were localized in the nucleus. Our study represents a pioneering effort in the systemic analyses of FveNF-Y genes and will be useful in understanding the functional characterization of NF-Y genes in Fragaria species. Full article
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22 pages, 25106 KiB  
Article
Comparative Metabolomic and Transcriptomic Analysis Reveals That Variations in Flavonoids Determine the Colors of Different Rambutan Cultivars
by Jiaqi Wang, Wencan Zhu, Chengkun Yang, Maofu Li, Shun Feng, Lizhu Tang, Chengchao Yang and Zhifu Cui
Horticulturae 2024, 10(3), 263; https://doi.org/10.3390/horticulturae10030263 - 10 Mar 2024
Cited by 1 | Viewed by 1608
Abstract
Rambutan is a tropical tree and its fruit has several favorable characteristics. To understand how the color of the rambutan fruit peel develops, the transcriptome, flavonoid metabolome, and carotenoid metabolome data of two rambutan cultivars, ‘BY2’ and ‘BY7’, which show yellow and red [...] Read more.
Rambutan is a tropical tree and its fruit has several favorable characteristics. To understand how the color of the rambutan fruit peel develops, the transcriptome, flavonoid metabolome, and carotenoid metabolome data of two rambutan cultivars, ‘BY2’ and ‘BY7’, which show yellow and red peels at maturity, respectively, were comprehensively analyzed at three developmental stages. We identified 26 carotenoid components and 53 flavonoid components in these cultivars. Anthocyanins were the main component contributing to the red color of ‘BY7’ after reaching ripeness. The carotenoid content decreased sharply as the fruit matured. Hence, we speculated that flavonols were the main contributors to the yellow color of the ‘BY2’ peel. In total, 6805 differentially expressed genes were screened by transcriptome analysis; the majority of them were enriched in metabolic pathways and the biosynthesis of secondary metabolites. Weighted gene co-expression network analysis results revealed that in addition to MYB and bHLH, ERF, WRKY, MYB-related, and C3H were the main potential transcription factors regulating the color of the rambutan peel. In addition, we also identified 12 structural genes associated with flavonoid biosynthesis. The research findings shed light on the molecular mechanisms of color acquisition in rambutan fruit peels, laying the foundation for the quality control of rambutan and the cultivation of differently colored cultivars of rambutan. Full article
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2023

Jump to: 2025, 2024, 2022

19 pages, 11813 KiB  
Article
Physiological and Transcriptional Analysis Provides Insights into Tea Saponin Biosynthesis and Regulation in Response to SA in Camellia vietnamensis Huang
by Yang Li, Heqin Yan, Muhammad Zeeshan Ul Haq, Ya Liu, Yougen Wu, Jing Yu and Pengguo Xia
Horticulturae 2024, 10(1), 8; https://doi.org/10.3390/horticulturae10010008 - 20 Dec 2023
Cited by 2 | Viewed by 1735
Abstract
Camellia vietnamensis Huang is an important and famous woody oil crop with high economic value in China because of its high-quality, edible, and medicinal oil. As one of its major active components, tea saponin (triterpenoid saponin) has shown anticancer, antioxidant, bacteriostatic, and other [...] Read more.
Camellia vietnamensis Huang is an important and famous woody oil crop with high economic value in China because of its high-quality, edible, and medicinal oil. As one of its major active components, tea saponin (triterpenoid saponin) has shown anticancer, antioxidant, bacteriostatic, and other pharmacological activities. In this study, C. vietnamensis was used as an experimental material to determine the tea saponin content and physiological activity indicators after salicylic acid (SA) treatment and to analyze the differential expression genes of key metabolic pathways in response to SA by combining transcriptome data. The results showed that SA treatment increased the content of tea saponin and total phenols in leaves; effectively promoted the activity of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX); and decreased the content of malondialdehyde (MDA). A total of 60,038 genes, including 5871 new genes, were obtained by the RNA-seq. There were 6609 significantly differential expression genes mainly enriched in pathways such as sesquiterpenoid and triterpenoid biosynthesis, terpenoid backbone biosynthesis, diterpenoid biosynthesis, and flavonoid biosynthesis. The SA-induced key structural genes (SQS, SQE, bAS, CYP450, and UGT) and transcription factors related to the tea saponin biosynthetic pathway were screened by weighted gene co-expression network analysis (WGCNA). The results of this study could provide a theoretical basis and a new technical method to improve the content of tea saponin, with its excellent anticancer activity, in C. vietnamensis. Full article
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13 pages, 4120 KiB  
Article
Transcription Regulation of Anthocyanins and Proanthocyanidins Accumulation by Bagging in ‘Ruby’ Red Mango: An RNA-seq Study
by Wencan Zhu, Hongxia Wu, Chengkun Yang, Xiaowen Wang, Bin Shi, Bin Zheng, Xiaowei Ma, Minjie Qian, Aiping Gao and Kaibing Zhou
Horticulturae 2023, 9(8), 870; https://doi.org/10.3390/horticulturae9080870 - 31 Jul 2023
Viewed by 2048
Abstract
The biosynthesis of anthocyanins and proanthocyanidins (PAs), components of two main flavonoids in plants, is regulated by environmental factors such as light. We previously found that bagging significantly repressed the biosynthesis of anthocyanins in red ‘Ruby’ mango fruit peel, but induced the accumulation [...] Read more.
The biosynthesis of anthocyanins and proanthocyanidins (PAs), components of two main flavonoids in plants, is regulated by environmental factors such as light. We previously found that bagging significantly repressed the biosynthesis of anthocyanins in red ‘Ruby’ mango fruit peel, but induced the accumulation of PAs. However, the molecular mechanism remains unclear. In the current study, transcriptome sequencing was used for screening the essential genes responsible for the opposite accumulation pattern of anthocyanins and PAs by bagging treatment. According to weighted gene co-expression network analysis (WGCNA), structural genes and transcription factors highly positively correlated to anthocyanins and PAs were identified. One flavanone 3-hydroxylase (F3H) and seven structural genes, including one chalcone synthase (CHS), one flavonoid 3’-hydroxylase (F3’H), one anthocyanidin synthesis (ANS), three leucoanthocyanidin reductase (LARs), and one UDP glucose: flavonoid 3-O-glucosyltransferase (UFGT), are crucial for anthocyanin and PA biosynthesis, respectively. In addition to MYB and bHLH, ERF, C2H2, HD-ZIP, and NAC are important transcription factors that participate in the regulation of anthocyanin and PA biosynthesis in ‘Ruby’ mango fruit peel by bagging treatment. Our results are helpful for revealing the transcription regulation mechanism of light-regulated mango anthocyanin and PA biosynthesis, developing new technologies for inducing flavonoid biosynthesis in mangos, and breeding mango cultivars containing high concentrations of flavonoids. Full article
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18 pages, 5564 KiB  
Article
TCP Transcription Factors in Pineapple: Genome-Wide Characterization and Expression Profile Analysis during Flower and Fruit Development
by Ziqiong Li, Yanwei Ouyang, Xiaolu Pan, Xiaohan Zhang, Lei Zhao, Can Wang, Rui Xu, Hongna Zhang and Yongzan Wei
Horticulturae 2023, 9(7), 799; https://doi.org/10.3390/horticulturae9070799 - 13 Jul 2023
Cited by 4 | Viewed by 1877
Abstract
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors contain specific a basic helix–loop–helix structure, which is a significant factor in the regulation of plant growth and development. TCP has been studied in several species, but no pineapple TCP has been reported to date. Whether they are involved [...] Read more.
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors contain specific a basic helix–loop–helix structure, which is a significant factor in the regulation of plant growth and development. TCP has been studied in several species, but no pineapple TCP has been reported to date. Whether they are involved in the development of the flower and fruit in the pineapple remains unclear. In this study, nine non-redundant pineapple TCPs (AcTCPs) were identified. Chromosomal localization, phylogenetics, gene structure, motifs, multiple-sequence alignment, and covariance on AcTCP family members were analyzed. Analysis of promoter cis-acting elements illustrated that the AcTCP gene may be mainly co-regulated by light signal and multiple hormone signals. Analysis of expression characteristics showed a significant increase in AcTCP5 expression at 12 h after ethylene treatment, and significantly higher levels of AcTCP8 and AcTCP9 expression in the pistil than in other floral organs. Meanwhile, the AcTCP4, AcTCP5, AcTCP6, AcTCP7, and AcTCP9 expression levels were downregulated at later stages of fruit development. Transcription factors that may interact with TCP protein in the regulation of flower and fruit development are screened by the protein interaction prediction network, AcTCP5 interacts with AcSPL16, and AcTCP8 interacts with AcFT5 and AcFT6 proteins, verified by Y2H experiments. These findings provide a basis for further exploration of the molecular mechanisms and function of the AcTCP gene in flower and fruit development. Full article
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2022

Jump to: 2025, 2024, 2023

17 pages, 20220 KiB  
Article
Genome–Wide Investigation of the CBL–CIPK Gene Family in Oil Persimmon: Evolution, Function and Expression Analysis during Development and Stress
by Cuiyu Liu, Yanpeng Wang, Jin Yao, Xu Yang, Kaiyun Wu, Guoxin Teng, Bangchu Gong and Yang Xu
Horticulturae 2023, 9(1), 30; https://doi.org/10.3390/horticulturae9010030 - 27 Dec 2022
Cited by 3 | Viewed by 2115
Abstract
Ca2+-sensors, calcineurin B-like proteins (CBLs), and calcineurin B-like protein-interacting protein kinases (CIPKs) form a CBL–CIPK complex to regulate signal transduction. This study aimed to reveal the characteristics of the CBL–CIPK gene family in oil persimmon (Diospyros oleifera). Ten DoCBL [...] Read more.
Ca2+-sensors, calcineurin B-like proteins (CBLs), and calcineurin B-like protein-interacting protein kinases (CIPKs) form a CBL–CIPK complex to regulate signal transduction. This study aimed to reveal the characteristics of the CBL–CIPK gene family in oil persimmon (Diospyros oleifera). Ten DoCBL and 23 DoCIPK genes were identified, and gene duplication among them was mainly attributed to segmental duplication. According to phylogenetic and structural analysis, DoCBLs were clustered into four groups with distinct motifs, namely myristoylation and palmytoylation sites in their N-terminus, and DoCIPKs containing a NAF/FISL domain were clustered into intron-rich and intron-less groups. The expression patterns of DoCBLs and DoCIPKs were tissue- and time-specific in different tissues and at different stages of fruit development. Most CBL–CIPK genes were upregulated under NaCl, drought, and Ca(NO3)2 stress using qRT-PCR analysis. DoCBL5 and DoCIPK05 were both located in the plasma membrane of cells using green fusion proteins (GFP) in tobacco leaves. DoCBL5 and DoCIPK05 might interact with AKT1, PP2C, and SNF to regulate the Ca2+ signals, K+, and ABA homeostasis in cells. In conclusion, these results suggested that the CBL–CIPK family genes might play important roles in oil persimmon growth and stress responses. Full article
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